Metroid Prime 3: Corruption
by sirkibble2
Summary: Samus' most debilitating adventure against the threat of Phazon. The Space Pirate Commander is drafting a plan to attack the Valhalla while the Galactic Federation prepares the prototype PED's. Ridley is none to happy about the commander's inactivity.
1. Allies

**_A/N: This is my first foray into the world of fan fiction in a long time. Unfortunately, I wasn't able to get anyone to look at this in decent time so I'm hoping the amounts of beta reads I did had a decent job. My biggest problem is dialogue descriptions so any help is appreciated for that specifically. Hope you enjoy it!_**

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_Allies_

"We have mined out all the ore left by the Galactic Federation, sir," a Space Pirate miner noted.

"Excellent. With this, we will have enough Phazon to execute our attack against the Galactic Federation. They were considerably foolish to leave any amounts of Phazon for us to take," the Space Pirate Commander said confidently.

Aether had been liberated not only from Space Pirates and Phazon, but from an alternate dimensional force known as the Ing. The Ing were formed by Phazon corruption creating an alternate dimension of the planet and thus, creating an alternate species to the Luminoth. The Luminoth were beings of light and the Ing were beings of Dark. After Samus defeated Dark Samus, the Ing and their alternate dimension were destroyed although some Phazon remained on the planet.

The Galactic Federation stayed for a while and mined some of the Phazon but left some behind which the Space Pirates mined out.

The Space Pirate Commander spoke up again to the miner. "Take this Phazon straight to the Klar Nebula. There you will find a Galactic Federation training vessel. I will send my troops along with you to attack the vessel. Once we have completed the attack on the vessel, plant a Phazon virus into their organic supercomputer. Do you understand this?"

"Yes, sir," the miner saluted.

"Good," the commander smirked.

=.=.=.=

Sirens blared and engines roared in the raiding vessel as the Space Pirate raiding troops were preparing for battle. They were fast approaching the Galactic Federation vessel with a ship that was far smaller than the Federation flagship. This was not the only ship readying for battle.

"Commander, we are approaching the Federation ship, _Valhalla," _a Pirate raiding troop warned.

"That is the ship we are going to attack," the commander said sternly. He moved to a large platform where some other pirates were executing commands on their computers. He stood confidently and silenced the alarms and lifted his hands to grab attention of his troops. The Pirates slowly directed their attention to them.

"Space Pirates!" he yelled, his voice echoing and the noise dying down. "This will be the beginning of the end of the Galactic Federation. When we attack this vessel, leave no one behind! Leave no one standing! Kill them all!! We will not be opposed any longer! We are the Space Pirates and WE WILL HAVE OUR VICTORY!!!"

Loud roars erupted from the troops and the commander stood and let them revel for a bit. He motioned his arms up and down to bring down the noise. It quickly got quiet.

"The _G.F.S. Valhalla _is heavily armed," he started. "In order for us to execute this attack with success, we will have to be quick, precise and efficient. I will send our most elite troops. I will not allow any mistakes for this mission. If anything goes--" the commander was suddenly interrupted by one of the men at the computer terminals.

"Commander! Red alert upon the mining ship! There's seem to be a problem in the Phazon containment room!"

"What?! Did a GF vessel attack us?" he asked with shock all over his face.

"No sir. I believe it is something worse..."

The Commander ran to the computer screen. The troops below stood frozen as he looked at the screen examining the situation. The commander's eyes widened. When the troops saw this, they began to speculate among themselves.

"It can't be... we are cursed!" the commander exclaimed. "Quick, get me a ship! I need to get over to the vessel!"

=.=.=.=

The Pirates were on their knees hoping for mercy. There was no begging for them. Dark Samus loomed over them--her gun pointed at one pirate but it seemed like she could destroy all of them with one blast. Phazon crates laid broken all over the room. A bright blue glow emanated from Dark Samus lighting up the lightless room.

Outside of the mining ship, the commander landed his ship on the vessel. He rushed out of his ship and into the vessel immediately going for the Phazon containment room. Dashing through the halls as fast as possible he was met by Dark Samus who whizzed right in front of him. The power of Phazon vapor from Dark Samus flung him back a few feet to his backside.

He laid there frozen in fear.

"N-no... It can't be... I th-thought The Hunter finished you...." the commander stuttered frighteningly. Dark Samus did not say a word but pointed her gun to his head.

"Wait!" the commander exclaimed in fear. He slowly began to rise to his feet. "Wait." He stood trying to gain his composure. "Since you are alive I can make you a proposition." He could feel his stomach knotting up tighter and tighter every second. He could not believe he was about to make a proposition with Dark Samus. It was the only chance he had left or else he would and the rest of the Space Pirates would be obliterated. Dark Samus had no ally as was shown back on the Chozo habitation Tallon IV.

"We both hate The Hunter," he snarled. "Because of her, we have not successfully mined any Phazon, up until now. With your help, we can be rid of the Galactic Federation, mine more Phazon and create a galaxy full of it!" his eyes glowed at the thought of colossal amounts of Phazon. "In return for your help, we, the Space Pirates, will give our allegiance to you. We know you hunger for Phazon and we want to fulfill that hunger. The only ones who oppose Phazon is the Galactic Federation and Samus. We will help you."

Dark Samus stood a few inches above the ground giving what looked like the stare of death to the commander. The high ranked Space Pirate imagined the quick, painful death he could possibly get from Dark Samus if she decided not to go along with it. Another moment passed and to his surprise and relief, she slowly lowered her gun. She actually complied with his request. She slowly moved toward the Phazon containment room where the miners were still writhing in fear.

The commander took a look at the room. The Phazon containers were completely destroyed and there were no traces of the Phazon left. Dark Samus absorbed it all. The commander looked at the room seeing the debris and the the Miner Pirates shaking heavily. The commander walked passed the other pirates, stood and looked at them.

"Get up. We have allied with Dark Samus," he said reassuringly. The pirates looked at each other in dismay. Could they really be under the orders of Dark Samus now? Apparently so. They all rose as the commander told them to. "Do not be afraid. She will not harm us but we will submit our total allegiance to her. Understood?"

They all nodded without a second thought. The commander walked passed them and passed Dark Samus. He could feel the Phazon radiation coming out of her as if he was in a pool of it. It made him shudder. He was glad he did what he did. He activated the intercom on his gun which sent a transmission to the raiding ship.

"Space Pirates!" the commander yelled over the intercom. All the troops on the ship jolted to attention hearing the voice over the intercom. "Everything on the mining vessel is under control. Please make your way to the vessel. I actually have a pleasant surprise that will ensure victory of our attack!"

The commander switched off his intercom, looked at Dark Samus and Dark Samus approvingly stared back at him. The commander knew what he had done would surely give him victory against Samus and the Galactic Federation and high honor with the Space Pirate Command.


	2. Arrival

**A/N: After writing my first chapter and getting little reviews, little inside or outside help, I decided to hold back my other chapters figuring there was little interest. I don't write these just for me--that's boring. I know I enjoy my writing. It's nice to know others do. And that's why I have posted this chapter. I know at least one person has interest in the story, so I've decided to continue. **

**Hope others enjoy this also. Here goes!**

_Arrival_

The events of Aether changed everything. After what transpired on the peaceful planet, the Galactic Federation knew it was time to make the threat of Phazon their top priority. The hunt was no longer about stopping the Space Pirates, it was about stopping what became the greatest threat known to every galaxy--even greater than the Metroids. Phazon had the capacity to mutate, cripple, transform, tear apart and most critically, kill. Where this Phazon came from continued to elude the Galactic Federation but wherever it had been, the Space Pirates were there mining out the substance.

After Aether, the GF found an abandoned Space Pirate mining facility and recovered several amounts of Phazon ore. Foolishly, they also left large amounts of unmined Phazon and the Space Pirates recovered what was left. The threat of Dark Samus was still unresolved. The Galactic Federation was aware that Samus defeated the Phazon incarnation but since Phazon still exists, the Federation cannot count out the probability of Dark Samus still existing--who was birthed out of Phazon thorough Metroid Prime.

Traveling along the outskirts of a large blue planet filled with a dense amounts of clouds, the _G.F.S. Olympus_ hovered above while other smaller ships circled making their rounds to and from the other military vessels. The ship was comprised of several docking bays, weapon containment rooms, special facility spaces and a room specifically for the ships organic supercomputer. This was the Galactic Federations most elite flagship.

Inside the hull, many men were at their computers monitoring the ships' actions and some were monitoring the actions of the planet below. Norion, the blue planet similar to Earth in ways, was where the GF had chosen to station themselves as the primary point to finding the source of Phazon. It, and the other planets were found to have no traces of Phazon but Norion was chosen as their base of operations.

"Any sign of her?" a man asked with a gruff voice. He was dressed in forest green military attire outfitted with a button over shirt, thick combat slacks, combat ready boots and a large green hat that covered his forehead. He was a hard looking man and was of upper age signified by the wrinkles in his cheeks and above his brow. His eyes were naturally squinted adding to his rough appearance.

"No, sir. No sign of her yet," the young ship coordinates mate answered back.

"Hurry up Samus..." the hardened man murmured to himself.

The man walked back to a room that was dimly lit. Inside were four ship crewmen who took care of manual security measures on their specific computers. They were the men hard at work making sure their ship, the _G.F.S. Olympus_, remained well in order. There was also a large projector in the middle of the room mounted in the floor. This is where the organic supercomputer revealed itself. The hardened man, looked at his crew and turned to other alien creatures who were also in the room.

"Where is she, Admiral? She should have been here by now. She has been under your payroll for some time. You would think she would be a little more timely," a cold voice remarked.

"Yes, but she can be cautiously slower about things. She has more on her plate than most hunters. Besides, one of my other hunters is still on the way also," the general replied.

"I see. Well--" a voice from the general's com interrupted the cold voice.

"Sir. We have an unidentified ship on our radar," the voice said quickly.

"Good. It's probably Samus. Run through the procedures."

"Yes, sir."

Inside Samus' ship were several command controls. She moved her ship into position and hovered there until she received communication from the Galactic Federation. A deep voice over her intercom came into transmission.

"Unidentified ship. Please switch to a secure radio frequency and transmit your identity code. We will be standing by."

She immediately reached for her controls that activated her radio transmitter. Above her head at the top of her windshield hung the radio transmitter. She activated it at the press of a button on her panel and it slowly rotated down and opened itself revealing a screen and several transmission character panels sticking out the edge of the screen. She quickly tapped in her identity code and the screen retreated back to its original position.

The voice came back in through her com. "We have received your identity code. Welcome aboard the _Olympus, _Samus. You can dock in bay number 5."

"Copy that," she replied.

She switched her ship out of hovering, reactivated her thrusters and docked her ship into the _Olympus._


	3. Plan

**A/N: Computers are amazing but they can be a pain in the butt. My computer that I had my save file on for this chapter pretty much stopped working. My word processing program would not open and the file I had saved it with was an exclusive file to the Mac program Pages. I had to wait until I got to another Mac computer with Pages and I finally did. That has been the cause of this extensive delay. But the story is here now and there will be same major revisions in the near future that you will notice. I apologize for the delay but here's the next chapter. R&R  
**

_Plan_

There seemed to be a different persona about the Pirate Commander. He walked straighter, there was a greater sense of peace, but even more so than anything, he looked bolder. Dark Samus was now allied with the Pirates and one of two feelings showed with the other Pirate troops--confidence or fear. If there was fear, it was because they had no idea what they were dealing with. To put faith into the being that would stop at nothing to get what she wanted seemed maniacal. If there was confidence, it was because of the power their new ally possessed.

Outside of the mining vessel, the Space Pirate starship crept behind it looking for the best position to board the mining vessel. The starship was massive. It was outfitted with turrets, several docking bays and plasma cannons. It was the direct counter to any GF starship. After a moment of repositioning, the starship casually slid next to the mining vessel and a giant ramp opened up onto the small docking bay. Swarms of Pirates walked out of the ship not knowing what to expect from their commander. The message he left with them was vague.

Suddenly, a door opened to the docking bay port. The Commander was walking in. He had a slim helmet with a bright, single-eye on the front. His armor was made of extremely sturdy phazite, a hard crystallized form of Phazon, that was colored red. He walked casually toward his troops and they stood anxiously waiting for his order.

The Commander looked at them smirking beneath his helmet. The troops began looking at each other wondering why their commander seemed so proud.

The Commander chuckled to himself. "My fellow Pirates," he spoke calmly and confidently. "As I told you on the ship, I have found a way to guarantee our victory against the Galactic Federation. What happened in that Phazon containment room was actually a blessing in disguise."

The Pirate troops looked confused but they focused on the Commnader.

"While in the containment room, I found someone who I had no inclination of seeing," he paused. The Pirates began to speculate among themselves that Samus had been on board.

"Fear not. It was not The Hunter," he said brashly. "But, it is someone who can defeat The Hunter." He paused as he watched the Pirate faces grow curious. "Dark Samus," he finished.

The room became so quiet it seemed like no one was breathing. They stared at the Commander with mixed reactions. Some were awestruck, some were fearful, some were joyous. Dark Samus appeared next to the Commander in a bright display of glowing Phazon.

"Fear not. She is on our side. I told her if she would help us, we would give our total allegiance to her," he said smiling. His smile shortly faded as he began seeing the Pirates talk among themselves again.

"What? What is the matter?" the commander asked irritated and worried.

A trooper stepped forward. "Sir, we are proud to have such great power by our side and we are happy to do what you ask but we must ask, since this was done so quickly, has High Command been informed of this?"

The Commander glared at the trooper. How could they be so cynical when they have received the greatest gift that could be given them? There was nothing to be feared. He could understand their concern. To usurp High Command's authority would mean death. The Commander knew this but he could not pass up the opportunity. With this decision, he would probably be promoted to High Command.

"I understand your concerns troops, but there is no need to worry. High Command will not be upset at this decision. Anything that be rid of Samus, the Galactic Federation and anything that would gain us our prize of Phazon would be commended," he said confidently.

The troop who spoke stood for a moment confused but he nodded in submission. "Yes, sir. We trust your judgment. You would not be in the position you are in if you lacked it."

"Thank you."

=.=.=.=.=

Aboard the _Valhalla_, hundreds of GF trainees were doing vigorous workouts as they were making their way to the GF training base. The _G.F.S. Valhalla _was an enormous ship. It was the prototype to the _G.F.S. Olympus _which would be scheduled to be completed in a month.

Inside the ship, special scientific research going on. Phazon containers were strewn about the room while scientists punched in numbers on their computers. In the middle of the room was an empty GF armor suit, hovering in the research tube, and something that looked like an armored chest plate that glowed a bright blue attached to it.

"Chief, the data analysis is complete. The Phazon Enhancement Devices should be working," a woman said.

"Good. We're going to have to take this back to the _Olympus _and quickly. Is there anyway we can test this technology?"

"Yes..." she replied hesitantly. "It could be dangerous though."

"Well, I thought you said the PED's should be working. They are working right?" the chief was getting impatient. The Chief of Military Science oversaw all the work that went into Galactic Federation equipment. That included ships, armor and weaponry.

"Well, yes. On paper it works but just as you suggested, we're going to have to test this technology. There is great risk in using Phazon and it could be fatal if anything were to go wrong. I understand that we do not want to get this technology into Pirate hands but--" she was abruptly interrupted.

"Listen! The Pirates are looking for us and they are leaps and bounds ahead of us in Phazon technology! They have been mining it, studying it and have been using technology like this since we have first found Phazon! Remember the Omega Pirate Samus told us about?" He did not give her a chance to answer. "That is a prime example of what those Pirates are up to. With what they gathered on Aether recently--"

"They gathered Phazon on Aether?" the scientist interrupted in astonishment.

The chief sighed. "Yes. We just got reports back that there was Phazon left over. We had never mined the stuff before. They knew exactly what to look for. Those bastards..."

The chief clenched his fist angrily.

The woman placed a comforting hand on his arm. "Sir, I understand your concerns but we are going to have test the PED's...with a living body. Without a living body, it will be hard to tell under what different circumstances can affect the PED. We have to factor emotion, weight, diet, among other things" the woman said compassionately.

"Yes, I know," the chief said still irritated at the whole situation. "I know this must be done. Even I want to skip steps but I don't want to put our troops at risk."

The scientist stared at the chief. The chief looked at her confused.

"Sir, this whole project is a risk."

=.=.=.=.=

The Pirate troops returned to the starship. The Commander was at work reforming his plan of attack. Now that Dark Samus was involved, he could potentially let her loose and destroy everything in site, but he still wanted this to primarily be a Pirate attack. If he let the Galactic Federation know that Dark Samus was involved with the attack, it could cause great fear in them but it could also cause them to prepare. Not to mention it would quickly get Samus involved. That is something the Pirates did not want.

A Pirate troop walked into the briefing room where the Commander was. A giant window revealed the beautiful stars of space giving a wondrous backdrop to the desk that the Commander sat at. Decoration was sparse save the Pirate emblem in the middle of the ground. Dark Samus was standing parallel to him.

"What is it?" the Commander demanded. "You know we are busy."

"I'm sorry sir, but I just received a transmission from Ridley and he would like to speak to you."

The Commander shot up in his chair. Could he have found out so quickly? He breathing was heavy.

"Is he here?" the Commander asked nervously.

"No, sir. It is a transmission," he repeated somewhat shocked. No matter who it was, the mention of Ridley struck fear in the minds of Pirates. He was a harsh leader and became even moreso when Samus took him down.

"I will be there immediately." The troop acknowledged and walked out the room. The Commander looked at Dark Samus. She gave no sign of returning any concern to him.

=.=.=.=.=

The room was very well lit by the transmission screen. It hung high on the wall so that many troops could see at once. The room was fairly smaller than some of the others on the starships holding about 50 troops at once. It was mostly used for Commando Pirates.

The Commander walked into the room and Ridley's face shown on the screen. His red eyes were always intimidating and it was always hard to tell what mood he was in until he spoke. This time, he sounded impatient.

"Yes, sir," the Commander bowed.

"What is taking so long. _Valhalla_ should have been destroyed by now. I have no time for games," he said irritated.

"There was a problem in the Phazon Containment Room on the mining vessel. The problem has been resolved and I am currently working on the plan of attack," he said reassuringly.

"You are just now working on the plan? If you would have figured that out earlier, you could have executed the attack and the problem with the Phazon would have never happened. Where are your coordinates?"

Arguing with Ridley was the last thing he wanted to do but he needed to do it. He did not want to let High Command know about Dark Samus's presence. He was going to have to do it though.

"Sir," he said calmly. "Allow me to explain the situation--."

"Where are the coordinates to your ship?" Ridley asked his eyes glowing redder.

"Please sir, let me explain." The transmission dropped. The Commander stared at the screen trying to figure what just happened. He got up quickly and tried to reset the connection but found that High Command was no longer available to be contacted. He darted outside to the Pirate technician on the nearest computer.

"What happened to the transmission?"

The technician could sense the fear on the Commander's face and began frantically figuring out what happened to the connection. The technician sat back in his chair and looked at the Commander.

"He dropped connection with you, sir," the technician said in the most calm way he could. The Commander did not take to the news as pleasantly as the technician did. Ridley would find the coordinates himself and now he would have to find out about Dark Samus the hard way. He would be killed and the mission for _Valhalla _would be given to someone else.

He went back to the briefing room. He would finish the plan until Ridley showed up. By then, he would hope he had a good enough plan that Ridley could execute. This could be the last plan the Commander drafted up.


End file.
